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<p>
This page is part of the <a href="spec_1.53E.jsp">DAS 1.53E specification</a>
</p> 
 
 <h2>Documentation DAS alignment service</h2>

<hr>

<h3><a name="alignment">Retrieve a pairwise or multiple alignment </a></h3>

<p>
<b>Version:</b>1.1 - Feb. 03. 2006<br/>
<b>Scope:</b> Reference servers.
<br/>
<br/>

<b>Reference:</b>
<jsp:include page="reference.jsp"/>

<b>Command:</b> <i>alignment</i>
<br/>
<br/>

<h3>Request Format:</h3>
<pre>

<i>PREFIX</i>/das/alignment?query=ID[&amp;subject=ID[RANGE]][&amp;rows=START-END][&amp;subjectcoordsys=COORDSYS]

</pre>
<br/>
<br/>

<p>
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<tr id="row1">
<td><b>Description</b>:</td>
	<td>This query returns one or all alginments that are available for the query.</td>
</tr>

<tr id="row2">
<td><b>Arguments</b>:</td>
<td>
<dl>

  <dt><b>query</b> (required; one) the id of the query.<br/>
  <br/>

  <dt><b>subject</b> (optional; one or more) the id of the alignment - subject. <br/>
  To be able to deal e.g. with large numbers of sequence <br/>

  alignments it is possible to request an accession code +/- a range<br/>
  of sequences around this sequence. by providing the optional RANGE<br/>
  <pre>:before,after</pre>  where <i>before</i> and <i>after</i> are integers defining a range. e.g<br/>

  <i>/das/pfam/alignment?query=PF00307&subject=P15498:5,5</i><br/>

  <dt><b>rows</b> (optional; one) request a certain range of<br/>
  alignments, in case of servers that provide multiple alignments.<br/>

  <dt><b>subjectcoordsys</b> (optional;one) request that the subjects <br/>

  belong to a particular coordinate system.  To get more help on coordinate systems please<br/> 
  proceed <a href="help_coordsys.jsp">here</a><br/><br/>


  <dd> To get a list of available alignments for <i>query</i> use the entry_points request.</dd>
</dl>
</td>
</tr>



<tr id="row1"><td><b>Response</b>:</td>

<td>
The response to the <i>dsn</i> command is the "DASALIGNMENT" XML-formatted document.
</td>
</tr>
</table>
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<br/>
<br/>

<h3>Response Format</h3>
<pre>
&lt;?xml version="1.0" standalone="no"?&gt;

&lt;dasalignment xmlns="http://www.efamily.org.uk/xml/das/2004/06/17/dasalignment.xsd" xmlns:align="http://www.efamily.org.uk/xml/das/2004/06/17/alignment.xsd" xmlns:xsd="http://www.w3.org/2001/XMLSchema-instance" xsd:schemaLocation="http://www.efamily.org.uk/xml/das/2004/06/17/dasalignment.xsd http://www.efamily.org.uk/xml/das/2004/06/17/dasalignment.xsd"&gt;
	&lt;alignment alignType="type" name="name" description="description" position="position" max="maximum" &gt;
	&lt;alignObject dbAccessionId="someid" objectVersion="version" intObjectId="internalId" type="objectType" dbSource="someSouce" dbVersion="version" dbCoordSys="coords"  &gt;
		&lt;alignObjectDetail dbSource="someSouce" property="property"&gt;
			<i>some details about the object. e.g. description, etc.</i> 
		&lt;/alignObjectDetail&gt; 
		&lt;sequence&gt;
			SEQUENCESEQUENCESEQUENCE
		&lt;/sequence&gt;	
	&lt;/alignObject&gt;

	&lt;score methodName="scorename" value="scorevalue"&gt;
	&lt;block blockScore="score" blockOrder="position"&gt; 	
		&lt;segment intObjectId="intObjectId" start="start" end="end" orientation="+"&gt;
			&lt;cigar&gt;9I5M10D&lt;/cigar&gt;
		&lt;/segment>
	&lt;/block&gt; 	
	&lt;geo3D intObjectId="intObjectId"&gt;

		&lt;vector x="xCoord" y="yCoord" z="zCoord"/&gt;
		&lt;matrix 
			   mat11="float" mat21="float" mat31="float" 
			   mat12="float" mat22="float" mat32="float"
			   mat13="float" mat23="float" mat33="float"/&gt;
	&lt;/geo3D&gt;	
	&lt;/alignment&gt;


&lt;/dasalignment&gt;
</pre>
  

<br/>
<br/>

<hr>

<h3>Example </h3>
<ul>
<li>1a4a alignment PDB - UniProt <a href="http://das.sanger.ac.uk/das/msdpdbsp/alignment?query=1a4a">http://das.sanger.ac.uk/das/msdpdbsp/alignment?query=1a4a</a></li>

<li>alignment ENSP - uniprot <a href="http://das.sanger.ac.uk/das/aliguniprotensp/alignment?query=ENSP00000329399">http://das.sanger.ac.uk/das/aliguniprotensp/alignment?query=ENSP00000329399</a></li>
</ul>


<h3>Detailed explanation:</h3>

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<table>

  
     
  <tr id="row2"> <td>Element:&lt;<b>dasalignment</b>&gt;</td> 
  <td> (required; one only) </td>
  </tr>

  <tr id="row2"> 
  <td></td>
  <td>The appropriate doctype and root tag is
  DASALIGNMENT. 
  </td></tr>

   <tr id="row1"><td>Element:&lt;<b>alignment</b>&gt; </td>
       <td>(required; one or more) everything below belongs to an alignment.</td></tr>
   <tr id="row1">
      <td>attribute:type</td>
      <td>(optional) the type of the alignment</td>
      </tr>
  <tr id="row1">
      <td>attribute:name</td>
      <td> (optional) the name of the alignment</td>
  </tr>
  <tr id="row1">
      <td>attribute:description</td>
      <td> (optional) a human readable description of this alignment</td>
  </tr>
  <tr id="row1">
      <td>attribute:position</td>
      <td> (optional) if multiple alignments (or ranges of alignments) 
      are returned, the position of this alignment</td>
    </tr>
    <tr id="row1">
      <td>attribute:max</td>
      <td> (optional) the total number of alignments available. (useful if a range of a multiple alignment is returend).</td>
	</tr>

   <!-- start of object -->
<tr id="row2"><td>Element:&lt;<b>alignObject</b>&gt; </td>
   <td>(required; two or more)
   A description of the objects that are aligned. 
   </td>
	
	</tr>
	
	<tr id="row2">
   <td>attribute:objectVersion</td>
   <td> (required) version of Object. e.g. CRC64 checksum for protein sequences.</td>
	</tr>
	<tr id="row2">
   <td>attribute:intObjectId</td>
   <td> (required) internal, unique name name for this object.
    This is used in the SEGMENT section to identify to which object an alignment belongs to.</td>
	</tr>
	<tr id="row2">
   <td>attribute:type</td>
   <td> (optional) a type for this object which currently has to be one of DNA, PROTEIN, STRUCTURE. </td>

 
	</tr>
	
	<tr id="row2">
    <!-- start dbRef -->
	<td>attributeGroup:dbRef</td>
	<td>This attribute group is used for referring to a database.
	</td></tr>
	<tr id="row2">
	<td>attribute:dbSource
	<td>(required).  The name of the database.
	</td></tr>
	<tr id="row2">
	<td>attribute:dbVersion
	<td>(required).  The version of the database.
	</td>
	</tr>
	<tr id="row2">
	<td>attribute:dbCoordSys
	<td>(optional).  The co-ordinate system used by the database.  This is not always <br/>
   the same as the database.  For example, Pfam uses UniProt as an underlying co-ordinate system.  <br/>
  Coordinate systems are
  defined at the <a href="http://das.sanger.ac.uk/registry/help_coordsys.jsp">DAS
  registration server</a>
	</td>
	</tr>
	<tr id="row2">	
	<td>attribute:dbAccessionId
	<td>(required).  The database entry accession id.  For example, SCOP have sunid, Pfam accessions(PF01020).
	</td>
	</tr>
    <!-- end dbRef -->

    
   <!-- end of object -->

   <tr id="row1">
   <td>Element:&lt;<b>sequence</b>&gt; </td> 
   <td>(optional; one) the sequence of this object. Clients generally should use the DAS - SEQUENCE request to get the seqeuence, so this is optional.</td>
	</tr>
	
   <tr id="row2">
   <td>Element:&lt;<b>alignObjectDetail</b>&gt; </td> 

	<td>(optional; zero or more) details about the object</td>
	</tr>

   <!-- begin of detail.inc-->   
   <tr id="row2">
	<td>attributeGroup:detail</td>
	<td>The following attributes are bundled together to form a group of attributes that are capable of describing additional information about a particular node.
	</td>
	</tr>
	<tr id="row2">
	<td>attribute:dbSource</td>
	<td>(required). The database where the information about this source orginates.</td>
	<tr id="row2">
	<td>attribute:property</td>
	<td>(required). A description of the CDATA.  For example, if you wanted to give an alternative id for a database, e.g. a UniProt ID , then the 
&lt;someDetail dbSource="UniProt" property="id"&gt;VAV_HUMAN&lt;/someDetail&gt;
	</td>
	</tr>
<!-- end of detail.inc-->

	<tr id="row1">
   <td>Element:&lt;<b>score</b>&gt;</td>
    <td>(optional; zero or more) a score for this alignment.
   an alignment can be described with several scores. each of the scores is described with the following 
   </td>
   </tr>
   
   <tr id="row1">
   <td>attribute:methodName</td> 
   <td>(required) the name of the score, e.g. number of equivlanet residues (eqr), e-value, etc.</td>
   </tr>
   
   <tr id="row1">
   <td>attribute:value</td><td> (required) the value of the score e.g. 99, 10e-22 , etc.</td>

   <tr id="row2">
   <td>Element:&lt;<b>block</b>&gt;</td>

    <td>(required; one or more) a block of the alignment. 
   an alignment can consist of one or more blocks. Often it will be only one block, since the CIGAR type of writing the alignment information allows to encode blocks.
	</td>
	</tr>
	
   <tr id="row2">
   <td>attribute:blockScore</td> 
   <td>(optional) some kind of score for a block</td>
	</tr>
   <tr id="row2">
   <td>attribute:blockOrder</td> 
   <td>(required) The number of block in the alignment.</td>
	</tr>
	
   <tr id="row1"><td>Element:&lt;<b>segment</b>&gt;</td>
   <td>&nbsp;</td>
	</tr>

   <!-- start region.inc-->	
   <tr id="row1">
	<td>attributeGroup:region</td>
	<td>The following attributes are bundled together to form a group of attributes that are capable of defining a region on something using a predefined co-ordinate system.
	</td>
	</tr>
	<tr id="row1">
	<td>attribute:start</td>
	<td>(optional). The start co-ordinate.</td>
	</tr>
	<tr id="row1">
<td>attribute:end</td>
<td>(optional).The end co-ordinate.</td>
</tr>
   <!-- end region.inc--> 
   <tr id="row1">
   <td>attribute:intObjectId</td>
   <td>(required). The internal ID of the object.</td>
	</tr>

   <tr id="row1">
	<td>attribute:orientation</td>
	<td>(optional). Strand of the object</td>
	</tr>

   
      <tr id="row2"><td>Element:&lt;<b>cigar</b>&gt;</td>
   <td> (optional). encoding of the alignment.
    The "cigar" string provides an efficient way to encode an
   alignment. 15M2D3I e.g. means that the 15 residues of the sequence
   are <b>M</b>atched (aligned), then there are 2 <b>D</b>eletions,
   followed by 3 <b>I</b>nsertions. Since in some situations the alignment will just consist of an aligned block, the cigar string is optional.
   If it is missing the alignment is ungapped and ranges from "start" to "end" of the <i>SEGMENT</i>.
   </td>
	</tr>
	
    <tr id="row1"><td>Element:&lt;<b>geo3D</b>&gt;</td>
    <td> (optional) geometrical operation on 3D object.  
   if the objects to be aligned are three dimensional objects this
   section defines how one of the needs to be shifted and rotated
   in order to be superimposed with the others.

	</td></tr>
	
	<tr id="row1">
   <td>attribute:intObjectId</td> 
   <td>(required) The internal ID of the object.
 	</td></tr>


   	<tr id="row2"><td>Element:&lt;<b>vector</b>&gt; </td>

   <td>(required, one) the shift vector
    the <b>x</b>,<b>y</b>, and <b>z</b> attributes are describing the shift vector.
	</td>
	</tr>
	
   	<tr id="row1"><td>Element:&lt;<b>matrix</b>&gt;</td>
   <td> the "container" for the rotation matrix elements.
	</td></tr>

   <tr id="row1">
   <td>attribute:mat11 - mat33</td> 
   <td>(required) The rotation matrix</td>
	</tr>


</table>
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